usage:  prog [options] <name of refinement directory> <iteration number>

This program will extract the necessary parameters from an EMAN2 refinement and create a card file (card.txt)
and a particle meta data file in the correct formats for FreAlign. 


The Eman2 refinement directory is refine_04 and the iteration you want to use within it is the 7th iteration:
e2refinetofrealign.py refine_04 7 

       [-] [-] [-] [- MODE] [-] [-] [-] [- RESLOW] [- RESHIGH] [- RREC]
       [- VERBOSE] [- PPID]
       [positionalargs ...]

Option Type Description
--version None show program's version number and exit
--mode str Mode to run FreAlign in: Mode 1 - Refinement and Reconstruction, Mode 3 - Simple Search and Refinement
--fbeaut None (T/F)Apply extra real space symmetry averaging and masking to beautify final map prior to output
--ffilt None (T/F)Apply Single Particle Wiener filter to final reconstruction
--fstat None (T/F)Calculate additional statistics in resolution table at end (QFACT, SSNR, CC, etc.). T Uses more than 50 percent more memory.
--reslow float Resolution of the data included in the alignment. This is the low resolution value. ex:200
--reshigh float Resolution of the data included in the alignment. This is the high resolution value. ex:25
--rrec float Resolution of reconstruction in angstroms. It is the resolution to which the reconstruction is calculated.
--rclas float High resloution limit used for classification
--thresh float Phase Residual cutoff. Particles with a higher phase residual will not be included in the refinement
--mass float The ~mass of the particle in kilodaltons
--interp str Type of interpolation: 0 - Nearest Neighbor, 1 - Trilinear Interpolation (More Time-Consuming)
--randomizemodel None Optionally randomize the phases of the initial model to this resolution (in Angstroms)
--imem str Memory Usage: 0 - Least Memory, 3 - Most memory
--verbose int Level of verbose; how much information do you want the program to output?(0-9)
--ppid int Set the PID of the parent process, used for cross platform PPID

For more information go to emanwiki/EMAN2/Programs/e2refinetofrealign.